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- PDB-7zq4: Crystal structure of photosynthetic glyceraldehyde-3-phosphate de... -

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Basic information

Entry
Database: PDB / ID: 7zq4
TitleCrystal structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Chlamydomonas reinhardtii (CrGAPA) complexed with NADP+ and the oxidated catalytic cysteine
ComponentsGlyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
KeywordsOXIDOREDUCTASE / Rossman-fold domain / Calvin-Benson cycle / oxidated cysteine
Function / homology
Function and homology information


supramolecular complex / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / reductive pentose-phosphate cycle / chloroplast / kinase binding / glucose metabolic process / NAD binding / NADP binding / identical protein binding
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-NDP / Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsFermani, S. / Zaffagnini, M. / Lemaire, S.D. / Falini, G. / Fanti, S. / Rossi, J.
Funding support Italy, 1items
OrganizationGrant numberCountry
Not funded Italy
CitationJournal: Redox Biol / Year: 2022
Title: Structural snapshots of nitrosoglutathione binding and reactivity underlying S-nitrosylation of photosynthetic GAPDH.
Authors: Mattioli, E.J. / Rossi, J. / Meloni, M. / De Mia, M. / Marchand, C.H. / Tagliani, A. / Fanti, S. / Falini, G. / Trost, P. / Lemaire, S.D. / Fermani, S. / Calvaresi, M. / Zaffagnini, M.
History
DepositionApr 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
R: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,45713
Polymers76,1392
Non-polymers2,31711
Water10,305572
1
O: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
R: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
hetero molecules

O: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
R: Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,91426
Polymers152,2794
Non-polymers4,63522
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Unit cell
Length a, b, c (Å)142.396, 147.327, 74.758
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11R-726-

HOH

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Components

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Protein , 1 types, 2 molecules OR

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic / NADP-dependent glyceraldehydephosphate dehydrogenase subunit A


Mass: 38069.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Oxidation of the catalytic cysteine / Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Cell: chloroplasts / Gene: GAPA / Production host: Escherichia coli (E. coli)
References: UniProt: P50362, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)

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Non-polymers , 5 types, 583 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 1.2-1.6 M (NH4)2SO4, 0.1 M Bicine pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 12, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→46.43 Å / Num. obs: 84958 / % possible obs: 98.4 % / Redundancy: 13 % / Biso Wilson estimate: 24.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.024 / Rrim(I) all: 0.086 / Net I/σ(I): 17.5 / Num. measured all: 1108041 / Scaling rejects: 452
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.7313.81.1976050943900.8970.3331.2431.896.8
9-46.4312.30.0581886630.9980.0140.05243.499.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.89 Å46.43 Å
Translation5.89 Å46.43 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RM4

1rm4


Resolution: 1.7→45.18 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 26.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2289 8160 5.01 %
Rwork0.2169 154837 -
obs0.2175 84144 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.52 Å2 / Biso mean: 31.5611 Å2 / Biso min: 12.44 Å2
Refinement stepCycle: final / Resolution: 1.7→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5243 0 141 572 5956
Biso mean--38.3 38.36 -
Num. residues----684
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.720.34562700.3435074534496
1.72-1.740.36292840.33855121540596
1.74-1.760.32072680.32265091535996
1.76-1.780.38022950.32555032532796
1.78-1.810.32762790.32155066534596
1.81-1.830.36372760.31665141541796
1.83-1.860.33042580.30365005526396
1.86-1.890.28332780.29855015529395
1.89-1.910.31022910.30035063535495
1.91-1.950.30073070.30194929523695
1.95-1.980.31752950.27735139543497
1.98-2.020.32142510.26395234548597
2.02-2.050.27972710.27055129540098
2.05-2.10.27112660.25245158542498
2.1-2.140.2632530.24335236548998
2.14-2.190.28352710.2335136540797
2.19-2.250.24832680.22425126539498
2.25-2.310.23162310.22655216544797
2.31-2.380.24732550.22265198545398
2.38-2.450.21552540.22655200545498
2.45-2.540.22722950.22375192548798
2.54-2.640.24562220.22865233545598
2.64-2.760.21572620.2275275553799
2.76-2.910.21552530.21425225547899
2.91-3.090.20772920.20965262555499
3.09-3.330.22222670.20215249551699
3.33-3.660.17482580.19055286554499
3.66-4.190.21952760.179952825558100
4.19-5.280.15722660.168453085574100
5.28-45.180.20893480.184852165564100

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